Select vertices based on other object (like boolean modifier)
Solved it myself now with a littles script I cobbled together based on zeffis answer to this: How to find if a point is inside a mesh?

import bpy, bmesh

def is_inside(p, max_dist, obj):
    # max_dist = 1.84467e+19
    point, normal, face = obj.closest_point_on_mesh(p, max_dist)
    p2 = point-p
    v = p2.dot(normal)
    return not(v &lt; 0.0)

obj = bpy.context.active_object
bowl = bpy.data.objects['bowl']
bpy.ops.mesh.select_all(action="DESELECT")

mesh=bmesh.from_edit_mesh(bpy.context.object.data)
for v in mesh.verts:
    p = obj.matrix_world * v.co
    if is_inside(p,1,bowl): v.select = True


This can be a little slow, but does the trick: